Hi Doug,

Thank you very much for your reply and help. If I am not doing cluster by cluster how I can know which cluster is which   when I overlay the file onto MNI152? Is the following correct I am not sure how to input (using which option) my sig.mgh from QDEC:

mri_label2vol   --temp MNI152_T1_1mm_brain.nii.gz   --reg $FREESURFER_HOME/average/mni152.register.dat   --fillthresh 0  --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh--hemi lh  --annot lh.aparc.annot   --o sig2MNI.nii

Many thanks, Antonella

________________________________ From: Douglas Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Monday, August 27, 2012 10:23 AM Subject: Re: [Freesurfer] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space

You should use mri_label2vol. If you want to do it label by label, then you need to convert the cluster annotation (the .annot file) into labels with mri_annotation2label. Or you can feed the annotation directly into mri_label2vol to create a segmentation volume. You don't need to specify a subject (but it you were, it would be fsaverage). Leave fillthresh at 0; the clusters cannot overlap. doug

On 8/27/12 4:17 PM, Antonella Kis wrote:

Hi,

I want to overlay  my QDEC clusters on the

connectivity maps in FSL  on the MNI ( this is the template I use for my connectivity maps). I am not sure how I can mention the label of my clusters, the uncorrected clusters.

Should I use the sig.mgh as subject id, my clusters

were obtained from all my subjects or it should be the fsaverage? Should I use mri_label2vol or mri_surf2vol?

How I can identify the

label of my clusters more exactly how I can keep only the clusters (name and size) from QDEC as in thefollowing table or

where I can find for

each QDEC's cluster the label so I can use it under --label option ?

mri_label2vol   --label ???   --temp

MNI152_T1_1mm_brain.nii.gz

--reg

$FREESURFER_HOME/average/mni152.register.dat

--fillthresh .5   --subject

/lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh --hemi lh

--o precentral-lh.nii

Also is the 0.5 the  threshold  I  need to use with mri_label2vol under option --fillthresh if I want to get  my uncorrected clusters? How can I do this if as below I have two clusters in the same region?

Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69

ClusterNo  Max   VtxMax

Size(mm2)   TalX   TalY   TalZ NVtxs Annotation

---------  ---   ------

---------   ----   ----   ---- ----- ----------

1   -3.8743

18231    944.60   -39.8    1.5   14.1 2631  precentral

2   -3.8065

47386    1445.46    -8.2   33.1   33.9 2421  superiorfrontal

3   -2.8630

158749    181.92   -12.7  -12.6   46.4  506  superiorfrontal

4   -2.7960

73670    222.37   -33.7    0.9    8.1  564  insula

5    2.7914

52279    204.80    -9.8  -98.6    4.6  248  pericalcarine

6   -2.7364

43605    173.45   -41.4  -79.2   21.8  288  inferiorparietal

7   -2.6316

17412    301.53   -38.3    5.6  -36.8  439  temporalpole

8    2.6050

150788     64.40   -24.0  -59.1   54.7  165  superiorparietal

9   -2.5570

106020     75.96   -22.8   -8.6   47.9  200  precentral

10   -2.5070

88002     66.59   -17.6  -31.2   37.8  198  posteriorcingulate

11   -2.4736

113974    181.87   -52.7  -10.3  -26.6  236  middletemporal

12   -2.4496

118370    142.88   -43.6  -18.0  -25.5  289  inferiortemporal

13   -2.3087

111885     55.43   -46.6  -36.2   -3.9  165  bankssts

14   -2.2179

153596     36.91   -11.3    3.4   42.0  103  superiorfrontal

15   -2.1861

145681     95.36   -11.3   60.1   19.1  147  superiorfrontal

16   -2.1733

29252     59.92   -42.6   37.5   -4.4   92  parstriangularis

17   -2.1689

155583     34.83   -45.3  -14.7  -11.2   87  superiortemporal

18   -2.1636

22443     27.76   -41.6  -79.0   -3.1   43  lateraloccipital

19   -2.1592

139736     21.75   -47.5  -25.1   37.0   61  postcentral

20   -2.0221

19174      4.10   -34.2   33.8   29.2    6  rostralmiddlefrontal

---

From: Douglas N Greve greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space

You can use

mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat

doug

On 08/21/2012 11:06

AM, Antonella Kis wrote:

...

Dear All,

Is possible to

overlap my QDEC clusters onto MNI_152_T1 _1mm_brain

...

template?

Thank you. Antonella

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